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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 19-41316728-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41316728&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41316728,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_052848.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC97",
"gene_hgnc_id": 28289,
"hgvs_c": "c.391C>T",
"hgvs_p": "p.Arg131Cys",
"transcript": "NM_052848.3",
"protein_id": "NP_443080.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 343,
"cds_start": 391,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000269967.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_052848.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC97",
"gene_hgnc_id": 28289,
"hgvs_c": "c.391C>T",
"hgvs_p": "p.Arg131Cys",
"transcript": "ENST00000269967.4",
"protein_id": "ENSP00000269967.2",
"transcript_support_level": 1,
"aa_start": 131,
"aa_end": null,
"aa_length": 343,
"cds_start": 391,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_052848.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000269967.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC97",
"gene_hgnc_id": 28289,
"hgvs_c": "c.484C>T",
"hgvs_p": "p.Arg162Cys",
"transcript": "ENST00000886246.1",
"protein_id": "ENSP00000556305.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 374,
"cds_start": 484,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886246.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC97",
"gene_hgnc_id": 28289,
"hgvs_c": "c.196C>T",
"hgvs_p": "p.Arg66Cys",
"transcript": "NM_001346100.2",
"protein_id": "NP_001333029.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 278,
"cds_start": 196,
"cds_end": null,
"cds_length": 837,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346100.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TGFB1",
"gene_hgnc_id": 11766,
"hgvs_c": "n.303-14008G>A",
"hgvs_p": null,
"transcript": "ENST00000598758.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000598758.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC97",
"gene_hgnc_id": 28289,
"hgvs_c": "c.*147C>T",
"hgvs_p": null,
"transcript": "ENST00000596882.1",
"protein_id": "ENSP00000470858.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 15,
"cds_start": null,
"cds_end": null,
"cds_length": 49,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596882.1"
}
],
"gene_symbol": "CCDC97",
"gene_hgnc_id": 28289,
"dbsnp": "rs551538141",
"frequency_reference_population": 0.00001983185,
"hom_count_reference_population": 0,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.000020529,
"gnomad_genomes_af": 0.0000131387,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5820832252502441,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.236,
"revel_prediction": "Benign",
"alphamissense_score": 0.344,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.561,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_052848.3",
"gene_symbol": "CCDC97",
"hgnc_id": 28289,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.391C>T",
"hgvs_p": "p.Arg131Cys"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000598758.5",
"gene_symbol": "TGFB1",
"hgnc_id": 11766,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "n.303-14008G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}